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Illinois public lands, which are owned or managed by various municipal bodies, counties, park districts, forest preserves, and state agencies, contain numerous important prehistoric and historic archaeological and paleontological sites. Under the Archaeological and Paleontological Resources Protection Act, the responsibility for the protection of these sites rests with the Preservation Services Division. All archaeological research and investigations on public lands require a permit from the Division. All paleontological excavations require a permit from the Division. The act also provides strict penalties for vandalism and theft of archaeological and paleontological resources.

A unique aspect of Illinois archaeology is its underwater and shipwreck resources. Illinois owns more than one million acres of the bed of Lake Michigan. Its waters contain hundreds of historic shipwrecks dating to Chicago's heyday as a major shipping port. Locating, inventorying, and researching these historic wrecks is an ongoing Division project that is being carried out in conjunction with local maritime and diving groups.

Under the act, standards are established to evaluate and certify professional archaeologists in the state. The Illinois State Museum and the Division maintain a statewide file of known archaeological and paleontological sites. Staff members also assist developers, contractors, and other government agencies with technical and legal advice on the preservation, protection, or scientific excavation of resources on public lands. Additionally, the Division has staff trained to assist law enforcement personnel in the collection of evidence and damage assessments during the investigation of looting and vandalism on public lands.

The Division also administers the Human Skeletal Remains Protection Act (20 ILCS 3440), which protects burials, burial markers (including Indian mounds), and burial artifacts from disturbance, including vandalism, defacement , destruction, sale, exchange, excavation, or removal. The law applies to all marked and unmarked graves that are more than 100 years old and located in cemeteries that are not registered or licensed with the Illinois Comptroller's office. Under this act all unregistered human remains and burial artifacts are held in trust ownership by the State of Illinois. A permit from the Illinois Historic Preservation Agency is required for any disturbance or removal, including archaeological investigations.